"No. No. No! Sorry, wasn't it obvious? The Dream Lord was me. Psychic pollen. It's a mind parasite. It feeds on everything dark in you. Gives it a voice, turns it against you. I'm nine-hundred-and-seven. Had a lot to go on."
The amount of self-loathing the Doctor has is dangerous.
"But those things he said about you. You don't think any of that's true?"
"...Amy, right now a question is about to occur to Rory, and, seeing how the answer is about to change his life, I think you should give him your full attention."
He hides it well, but once you see it it's so painfully obvious you wonder if you were blind before. It will consume him, you think, if he dwells on it for too long. And it all comes flooding back to you, the way he gets excited over all the littlest things, the way he pulls the craziest stunts. Anything to keep his mind off of a sin he committed in the past. He has seen so much hurt -in all the planets- and you think that he is so empathetic because he feels as if he should fix it. He thinks that he should fix everything, because he believes that he, the Doctor, the wonderful-kind-beautiful Doctor, is the root of all the misery in the universe. He can't stand to see children cry, and his sole purpose in life seems to be helping other people- whether it is to prevent what happened on his own planet from happening on others or to ask forgiveness, you don't know. What you do know is that in his mind he will never be forgiven.
"There was an old Doctor from Gallifrey
Who ended up throwing his life away
He let down his friends and—"
What was the end of that sentence, you wonder. What had the Doctor done so long ago that he still was running from?
"There's only one person in the Universe that hates me as much as you do."
You knew of the Daleks and the Cybermen and the Slitheen and how they hated the Doctor. Despised him to the very core. Yet still, according to the Doctor, the most hatred came from himself. The Doctor is a good man, you know this. He is gentle and kind and extraordinary. At worst, he is just a tad silly. And sometimes he forgets about you. But that's okay.
"He always leaves you, doesn't he? Alone in the dark. Never apologizes"
"He doesn't have to."
"That's good. Because he never will."
You wish you had known. You wish you had known because you want to be able to fix him. You wish you had known before.
"Save him. You save everyone. You always do. That's what you do."
"Not always. I'm sorry."
"Then what is the point of you?"
You think back on that moment, and, for the first time, you notice his face as he says it. The obvious anguish is so great, so saddening, that for the first time since you have known him, he looks his age. His true age. His face is one of an old man, who has seen so much hardship in the worlds that his face has grown accustomed to tears. And you know that it has. You have heard him mourning, at night in the TARDIS, when he thinks you are asleep. Crying for everyone he has lost. And in nine hundred years, all whom he has lost are with him, everyday, in his mind, whispering accusations that they wouldn't have, had they been there. The Doctor trusts his mind. And his mind tells him that he is horrible. But he isn't. That is one of the few things you are sure of. Because if the Doctor is horrible, then the rest of the universe must be so evil that Heaven is forever empty.
The Doctor is a good man. He is one of the best men you have ever met, or heard of, or read about. And if he doesn't know that, well then. It's up to you to teach him.